Question: KEGGSOAP: problem with get.pathways.by.genes()
0
10.3 years ago by
Julien Meunier30 wrote:
Hi everyone, I am trying to convert entrez id (mouse) to KEGG pathway using the keggsoap package, and having a hard time. get.genes.by.pathway(c("path:mmu04060")) would give me the following result: [1] "mmu:100044793" "mmu:100047704" "mmu:110542" "mmu:11477" "mmu:11479" ... However, the following get.pathways.by.genes(c("mmu:11479")) returns character(0) I also tested get.pathways.by.genes with the IL2 gene (entrez id 16183) involved in several pathways, calling the function with "16183", "mmu:16183" and other variations with the same result. The vignette mentioned they might be "problem on the server side" with get.pathways.by.genes(), and I googled without succes. Any ideas to get this function to work ? Thank you for your time, Julien PS: I known I can use KEGG.db or org.Mm.eg.db, or other locale packages but for some reason I would rather use an online query.
pathways convert keggsoap • 584 views
modified 10.3 years ago by Saroj K Mohapatra400 • written 10.3 years ago by Julien Meunier30
0
10.3 years ago by
Saroj K Mohapatra400 wrote:
Hi Julien: For some reason, if you use more than one gene, the function does return the pathways. > get.pathways.by.genes(c("mmu:11479")) character(0) > > get.pathways.by.genes(c("mmu:11479", "mmu:11477")) [1] "path:mmu04060" "path:mmu04350" Best, Saroj Julien Meunier wrote: > > > Hi everyone, > > I am trying to convert entrez id (mouse) to KEGG pathway > using the keggsoap package, and having a hard time. > > > get.genes.by.pathway(c("path:mmu04060")) > > would give me the following result: > > [1] "mmu:100044793" "mmu:100047704" "mmu:110542" "mmu:11477" > "mmu:11479" ... > > > > However, the following > > get.pathways.by.genes(c("mmu:11479")) > > returns character(0) > > > I also tested get.pathways.by.genes with the IL2 gene (entrez id 16183) > involved in several pathways, calling the function with "16183", > "mmu:16183" and other variations with the same result. > > The vignette mentioned they might be "problem on the server side" with > get.pathways.by.genes(), and I googled without succes. > > > Any ideas to get this function to work ? > > > Thank you for your time, > Julien > > > PS: I known I can use KEGG.db or org.Mm.eg.db, or other locale packages > but for some reason I would rather use an online query. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
Hi Saroj, Thank you for your reply. Yet, I am still puzzled by the behavior of get.pathway.by.genes() in KEGGSOAP: I have been running this session: > sessionInfo() R version 2.9.0 (2009-04-17) i386-apple-darwin8.11.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] KEGG.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 [4] AnnotationDbi_1.6.0 Biobase_2.4.1 RCurl_0.94-1 [7] KEGGSOAP_1.18.0 loaded via a namespace (and not attached): [1] SSOAP_0.4-6 XML_2.3-0 and the following code: My.entrez2pathid<-function(refseqid){ require(KEGG.db) stopifnot(is.character(refseqid)) v<-mget(refseqid,KEGGEXTID2PATHID,ifnotfound=NA) return(v) } v1<-My.entrez2pathid(c("16185","11652")) would give this result > v1 $16185 [1] "mmu04060" "mmu04630"$11652 [1] "mmu04010" "mmu04012" "mmu04150" "mmu04210" "mmu04370" "mmu04510" [7] "mmu04530" "mmu04620" "mmu04630" "mmu04660" "mmu04662" "mmu04664" [13] "mmu04910" "mmu04920" "mmu05210" "mmu05211" "mmu05212" "mmu05213" [19] "mmu05214" "mmu05215" "mmu05218" "mmu05220" "mmu05221" "mmu05222" [25] "mmu05223" whereas My.ksoap.entrez2pathid<-function(refseqid){ require(KEGGSOAP) stopifnot(is.character(refseqid)) v<-get.pathways.by.genes(refseqid) return(v) } v2<-My.ksoap.entrez2pathid(c("mmu:16185","mmu:11652")) returns > v2 [1] "path:mmu04630" Checking on the KEGG website, the refseq id 11652 is associated with a lot of pathways (those returned in "v1"). Does anybody knows why KEGGSOAp seems to fail to retrieve all the pathways ? Many thanks, Julien Saroj K Mohapatra wrote: > Hi Julien: > > For some reason, if you use more than one gene, the function does return > the pathways. > > > get.pathways.by.genes(c("mmu:11479")) > character(0) > > > > get.pathways.by.genes(c("mmu:11479", "mmu:11477")) > [1] "path:mmu04060" "path:mmu04350" > > Best, > > Saroj > > > Julien Meunier wrote: >> >> >> Hi everyone, >> >> I am trying to convert entrez id (mouse) to KEGG pathway >> using the keggsoap package, and having a hard time. >> >> >> get.genes.by.pathway(c("path:mmu04060")) >> >> would give me the following result: >> >> [1] "mmu:100044793" "mmu:100047704" "mmu:110542" "mmu:11477" >> "mmu:11479" ... >> >> >> >> However, the following >> >> get.pathways.by.genes(c("mmu:11479")) >> >> returns character(0) >> >> >> I also tested get.pathways.by.genes with the IL2 gene (entrez id 16183) >> involved in several pathways, calling the function with "16183", >> "mmu:16183" and other variations with the same result. >> >> The vignette mentioned they might be "problem on the server side" with >> get.pathways.by.genes(), and I googled without succes. >> >> >> Any ideas to get this function to work ? >> >> >> Thank you for your time, >> Julien >> >> >> PS: I known I can use KEGG.db or org.Mm.eg.db, or other locale packages >> but for some reason I would rather use an online query. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >
Perhaps v2 returns the common pathway between both genes? Saroj Julien Meunier wrote: > > Hi Saroj, > > > Thank you for your reply. Yet, I am still puzzled by the behavior of > get.pathway.by.genes() in KEGGSOAP: > > > I have been running this session: > > > sessionInfo() > R version 2.9.0 (2009-04-17) > i386-apple-darwin8.11.1 > > locale: > C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] KEGG.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 > [4] AnnotationDbi_1.6.0 Biobase_2.4.1 RCurl_0.94-1 > [7] KEGGSOAP_1.18.0 > > loaded via a namespace (and not attached): > [1] SSOAP_0.4-6 XML_2.3-0 > > > > and the following code: > > My.entrez2pathid<-function(refseqid){ > > require(KEGG.db) > stopifnot(is.character(refseqid)) > v<-mget(refseqid,KEGGEXTID2PATHID,ifnotfound=NA) > > return(v) > > } > > v1<-My.entrez2pathid(c("16185","11652")) > > > would give this result > > > > v1 > $16185 > [1] "mmu04060" "mmu04630" > >$11652 > [1] "mmu04010" "mmu04012" "mmu04150" "mmu04210" "mmu04370" "mmu04510" > [7] "mmu04530" "mmu04620" "mmu04630" "mmu04660" "mmu04662" "mmu04664" > [13] "mmu04910" "mmu04920" "mmu05210" "mmu05211" "mmu05212" "mmu05213" > [19] "mmu05214" "mmu05215" "mmu05218" "mmu05220" "mmu05221" "mmu05222" > [25] "mmu05223" > > > whereas > > My.ksoap.entrez2pathid<-function(refseqid){ > > require(KEGGSOAP) > stopifnot(is.character(refseqid)) > v<-get.pathways.by.genes(refseqid) > > return(v) > > } > > v2<-My.ksoap.entrez2pathid(c("mmu:16185","mmu:11652")) > > > returns > > > v2 > [1] "path:mmu04630" > > > > Checking on the KEGG website, the refseq id 11652 is associated with > a lot of pathways (those returned in "v1"). > > > Does anybody knows why KEGGSOAp seems to fail to retrieve all the > pathways ? > > > Many thanks, > Julien > > > > > > Saroj K Mohapatra wrote: >> Hi Julien: >> >> For some reason, if you use more than one gene, the function does >> return the pathways. >> >> > get.pathways.by.genes(c("mmu:11479")) >> character(0) >> > >> > get.pathways.by.genes(c("mmu:11479", "mmu:11477")) >> [1] "path:mmu04060" "path:mmu04350" >> >> Best, >> >> Saroj >> >> >> Julien Meunier wrote: >>> >>> >>> Hi everyone, >>> >>> I am trying to convert entrez id (mouse) to KEGG pathway >>> using the keggsoap package, and having a hard time. >>> >>> >>> get.genes.by.pathway(c("path:mmu04060")) >>> >>> would give me the following result: >>> >>> [1] "mmu:100044793" "mmu:100047704" "mmu:110542" "mmu:11477" >>> "mmu:11479" ... >>> >>> >>> >>> However, the following >>> >>> get.pathways.by.genes(c("mmu:11479")) >>> >>> returns character(0) >>> >>> >>> I also tested get.pathways.by.genes with the IL2 gene (entrez id 16183) >>> involved in several pathways, calling the function with "16183", >>> "mmu:16183" and other variations with the same result. >>> >>> The vignette mentioned they might be "problem on the server side" with >>> get.pathways.by.genes(), and I googled without succes. >>> >>> >>> Any ideas to get this function to work ? >>> >>> >>> Thank you for your time, >>> Julien >>> >>> >>> PS: I known I can use KEGG.db or org.Mm.eg.db, or other locale packages >>> but for some reason I would rather use an online query. >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >